Receptor
PDB id Resolution Class Description Source Keywords
4CP5 2.32 Å EC: 2.7.4.6 NDPK IN COMPLEX WITH (RP)-SPMPAPP DICTYOSTELIUM DISCOIDEUM TRANSFERASE
Ref.: ENZYMATIC SYNTHESIS OF ACYCLIC NUCLEOSIDE THIOPHOSP DIPHOSPHATES: EFFECT OF THE ALPHA-PHOSPHORUS CONFIG ON HIV-1 RT ACTIVITY. ANTIVIRAL RES. V. 117 122 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EOI A:1156;
F:1156;
E:1156;
D:1156;
C:1156;
B:1156;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 452 uM
463.238 C9 H16 N5 O9 P3 S C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1F3F 1.85 Å EC: 2.7.4.6 STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T- TRIPHOSPHATE.MG COMPLEX DICTYOSTELIUM DISCOIDEUM NUCLEOSIDE DIPHOSPHATE KINASE ANTI-HIV NUCLEOSIDE ANALOGUEPHOSPHORYLATION CH...O BOND TRANSFERASE
Ref.: STRUCTURAL BASIS FOR ACTIVATION OF ALPHA-BORANOPHOS NUCLEOTIDE ANALOGUES TARGETING DRUG-RESISTANT REVER TRANSCRIPTASE. EMBO J. V. 19 3520 2000
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
17 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
19 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
20 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
22 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (51)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3EVO - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3ELH - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
15 3GP9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3EJM - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 3FBB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
18 3EMT - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
19 3FCV - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
20 3EIC - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
21 3EVM - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
22 3B6B - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
23 3FCW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
24 2B8Q - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
25 3DKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
26 3DDI - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3FBE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 3ETM - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
29 3GPA - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
30 3ENA - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
31 3EM1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
32 3EE3 - CDP MG n/a n/a
33 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 3Q86 - GTP MG n/a n/a
35 3Q8U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 3Q8V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
37 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
38 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
40 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
42 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
43 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
45 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
46 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
47 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
48 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
51 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EOI; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 EOI 1 1
2 TNM 0.704225 0.957143
3 TNM MG 0.605263 0.810811
4 TNV MG 0.567901 0.810811
5 ARP 0.521739 0.657143
6 APS 0.521739 0.657143
7 EMA 0.494118 0.863014
8 5HG 0.4375 0.821918
9 9PP 0.404762 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1F3F; Ligand: D4T; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1f3f.bio1) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1F3F; Ligand: D4T; Similar sites found: 70
This union binding pocket(no: 2) in the query (biounit: 1f3f.bio1) has 56 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F8L GAL 0.02029 0.46715 None
2 4N7C AEF 0.02904 0.43116 None
3 3KMT SAH 0.03163 0.40072 None
4 3S9K CIT 0.03479 0.4636 1.69492
5 1BTN I3P 0.0276 0.45687 1.88679
6 3R51 MMA 0.01194 0.46453 1.93548
7 1WRA PC 0.04051 0.42358 1.93548
8 3QDY A2G GAL 0.00114 0.51214 2.0979
9 3QDT A2G GAL 0.003136 0.48866 2.0979
10 3QDY CBS 0.04067 0.42349 2.0979
11 1PX8 XYP 0.01243 0.43936 2.58065
12 4PPU TYR 0.04885 0.40623 2.58065
13 1JN2 SFP 0.00171 0.55699 3.22581
14 2EB5 OXL 0.01082 0.44764 3.22581
15 3U1T MLI 0.01765 0.44244 3.22581
16 2Z9V PXM 0.01751 0.42745 3.22581
17 2VDJ HSE 0.04481 0.4265 3.22581
18 1Y2W NAG 0.02348 0.43072 3.52113
19 2Q8H TF4 0.01132 0.46583 3.87097
20 1XX4 BAM 0.0305 0.44172 3.87097
21 3JQ3 ADP 0.01753 0.41902 3.87097
22 2Q1A 2KT 0.04718 0.41535 3.87097
23 2F2U M77 0.0352 0.40544 3.87097
24 3O2K QRP 0.04593 0.40021 4.21941
25 3SJ0 DXC 0.04889 0.41927 4.22535
26 3TKA CTN 0.006872 0.50947 4.51613
27 3ZPG 5GP 0.02309 0.44851 4.51613
28 3LTW HLZ 0.03109 0.42456 4.51613
29 1V6A TRE 0.02001 0.42928 4.81928
30 1XE7 GUN 0.01119 0.46609 5.16129
31 1I0Z OXM 0.01948 0.45265 5.16129
32 2XDQ MGX 0.04085 0.43456 5.16129
33 1ZZ7 S0H 0.01916 0.4256 5.16129
34 1QO0 BMD 0.03091 0.42469 5.16129
35 2HFK E4H 0.04019 0.41029 5.16129
36 3QP4 HL0 0.02757 0.40007 5.16129
37 1ULE GLA GAL NAG 0.03459 0.43263 5.33333
38 2OFE NAG 0.0286 0.4264 5.6338
39 2ZWS PLM 0.01098 0.48335 5.80645
40 2ZJF BSU 0.006228 0.43905 5.80645
41 4B9E FAH 0.02643 0.4333 5.80645
42 2JBH 5GP 0.03473 0.40939 5.80645
43 3GJB AKG 0.00479 0.44888 6.45161
44 1EB9 HBA 0.02972 0.40521 6.45161
45 1HSJ GLC 0.01608 0.4733 7.09677
46 3P3N AKG 0.01842 0.43604 7.09677
47 3CQ5 PMP 0.0278 0.41386 7.09677
48 1V7R CIT 0.02028 0.45893 7.74194
49 4LHM AZZ 0.006822 0.452 7.74194
50 1YOA FMN 0.01154 0.48205 8.1761
51 1T0S BML 0.0393 0.42961 8.3871
52 1Z44 NPO 0.0332 0.45409 9.03226
53 4F4S EFO 0.04523 0.40784 9.21053
54 1EYE PMM 0.03714 0.40096 9.67742
55 1DXY COI 0.04355 0.43299 10.3226
56 1Y42 TYR 0.0476 0.40677 10.9677
57 1ECM TSA 0.04163 0.40573 11.0092
58 1SC3 MLI 0.02873 0.437 11.6129
59 1Y7P RIP 0.003043 0.4752 12.2581
60 2GWD GLU 0.004383 0.45064 12.9032
61 2JFV FLC 0.04425 0.41677 12.9032
62 2NVK NAP 0.01338 0.43297 13.5484
63 2Y7G AAE 0.02563 0.40138 14.1935
64 1GJW MAL 0.0113 0.42753 15.4839
65 3I0O SMI 0.0178 0.43176 17.4194
66 4M51 BEZ 0.002936 0.49019 18.7097
67 4COQ SAN 0.03342 0.42297 19.3548
68 2Q09 DI6 0.01731 0.42334 21.2903
69 4RJK PYR 0.02702 0.45957 24.5161
70 3MAG 3MA 0.0179 0.46209 28.3871
Pocket No.: 3; Query (leader) PDB : 1F3F; Ligand: D4T; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1F3F; Ligand: D4D; Similar sites found: 86
This union binding pocket(no: 4) in the query (biounit: 1f3f.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F8L GAL 0.01121 0.46738 None
2 1UO5 PIH 0.03961 0.43522 None
3 2Y7P SAL 0.005853 0.43381 None
4 4JCA CIT 0.03179 0.43314 None
5 4N7C AEF 0.01487 0.43116 None
6 3UEC ALA ARG TPO LYS 0.04463 0.40732 None
7 3S9K CIT 0.004524 0.50035 1.69492
8 1BTN I3P 0.0112 0.47103 1.88679
9 1WRA PC 0.01213 0.43555 1.93548
10 3R51 MMA 0.04138 0.42013 1.93548
11 3QDY CBS 0.02122 0.42349 2.0979
12 3BY8 MLT 0.03989 0.40978 2.11268
13 1PX8 XYP 0.005795 0.43936 2.58065
14 1JN2 SFP 0.02477 0.47031 3.22581
15 2EB5 OXL 0.005136 0.44764 3.22581
16 3U1T MLI 0.008804 0.44244 3.22581
17 2Z9V PXM 0.005122 0.4364 3.22581
18 5RHN 8BR 0.0104 0.40208 3.47826
19 1Y2W NAG 0.01161 0.43072 3.52113
20 1C1L GAL BGC 0.01118 0.43731 3.64964
21 2QLX RM4 0.02548 0.41952 3.7037
22 1Y1A GSH 0.01319 0.46665 3.87097
23 2Q8H TF4 0.005819 0.46583 3.87097
24 1XX4 BAM 0.01644 0.44172 3.87097
25 2F2U M77 0.01625 0.40544 3.87097
26 4EXO PYR 0.04694 0.41141 4.10959
27 3O2K QRP 0.01111 0.41242 4.21941
28 3SJ0 DXC 0.02578 0.41927 4.22535
29 3TKA CTN 0.001154 0.521 4.51613
30 3ZPG 5GP 0.01228 0.44851 4.51613
31 1V6A TRE 0.003827 0.44767 4.81928
32 1I0Z OXM 0.01028 0.45265 5.16129
33 1XE7 GUN 0.01423 0.44509 5.16129
34 2XDQ MGX 0.02236 0.43456 5.16129
35 1ZZ7 S0H 0.008927 0.4256 5.16129
36 3F81 STT 0.03398 0.42476 5.16129
37 1QO0 BMD 0.01551 0.42469 5.16129
38 4M5P MLA 0.04653 0.42379 5.16129
39 2HFK E4H 0.01027 0.42287 5.16129
40 4M5P 23W 0.02902 0.42229 5.16129
41 1A5Z OXM 0.04193 0.41397 5.16129
42 1Y9Q MED 0.02813 0.41225 5.16129
43 4C6F DOR 0.01765 0.40392 5.16129
44 4C6F NCD 0.01765 0.40392 5.16129
45 3QP4 HL0 0.01171 0.40007 5.16129
46 1ULE GLA GAL NAG 0.01831 0.43263 5.33333
47 2OFE NAG 0.01429 0.4264 5.6338
48 2ZJF BSU 0.002595 0.43905 5.80645
49 2ZWS PLM 0.03784 0.43639 5.80645
50 4B9E FAH 0.01347 0.4333 5.80645
51 3GM5 CIT 0.02658 0.41344 5.80645
52 2JBH 5GP 0.01638 0.40939 5.80645
53 3DGB MUC 0.0146 0.40351 5.80645
54 3P7I P7I 0.002563 0.44983 6.45161
55 1EB9 HBA 0.01327 0.40521 6.45161
56 1HSJ GLC 0.007577 0.4773 7.09677
57 3P3N AKG 0.008985 0.43604 7.09677
58 3BHO B4P 0.03188 0.43307 7.09677
59 3I51 45C 0.0126 0.40614 7.09677
60 4JWX 1N4 0.02564 0.405 7.09677
61 1V7R CIT 0.011 0.45893 7.74194
62 4LHM AZZ 0.003082 0.452 7.74194
63 1YOA FMN 0.00321 0.49899 8.1761
64 1T0S BML 0.02095 0.42961 8.3871
65 3D2Y AH0 ALA FGA LYS 0.004449 0.40894 8.3871
66 1Z44 NPO 0.01893 0.45409 9.03226
67 1O9U ADZ 0.01511 0.44369 9.03226
68 2C5S AMP 0.0122 0.41497 9.03226
69 2ZJ5 ADP 0.03582 0.40263 9.67742
70 1Y42 TYR 0.0246 0.40582 10.9677
71 1MOQ GLP 0.007005 0.40167 10.9677
72 1ECM TSA 0.01987 0.40573 11.0092
73 1SC3 MLI 0.01507 0.437 11.6129
74 1Y7P RIP 0.03623 0.41728 12.2581
75 1W3R PYR 0.04221 0.41382 12.2581
76 2GWD GLU 0.001837 0.45064 12.9032
77 2JFV FLC 0.02267 0.41677 12.9032
78 2NVK NAP 0.006111 0.43297 13.5484
79 1GJW MAL 0.004872 0.42753 15.4839
80 1H0C AOA 0.03405 0.41323 16.129
81 3I0O SMI 0.008461 0.43176 17.4194
82 4M51 BEZ 0.001381 0.49019 18.7097
83 4COQ SAN 0.01684 0.42297 19.3548
84 2Q09 DI6 0.00783 0.42334 21.2903
85 4RJK PYR 0.03137 0.42054 24.5161
86 3MAG 3MA 0.009656 0.46209 28.3871
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